Spectral imaging methods have proven to be useful techniques for studying complex samples, and can be used in different fields including microscopy, animal imaging, industrial product analysis, forensic detection of document anomalies, and analysis of artifacts and artwork such as paintings. Spectral imaging methods can include assembling an image cube that includes multiple image planes. Individual image planes can correspond, for example, to images of a sample that are measured at different detection wavelengths and/or irradiated at different illumination wavelengths. The image planes can be derived from measurements of one or more properties of a sample, including absorption of incident light, reflection of incident light, fluorescence, and scattering of incident light. An image cube can include a relatively large number of image planes so that computer-based analysis methods are used to extract information from the cube.